Study design

The Microbial Metagenomics Analysis Center provides investigators evidence-based advice on study design considerations, sample collection and storage, selection of sequencing technology, and analytical approaches for microbiome research. The center also assists in the drafting of study protocols, statistical analysis plans, and grant submissions.

Bioinformatic processing of amplicon and shotgun metagenomic sequencing data

There has been an explosion in the development of accurate and efficient algorithms to generate taxonomic and functional profiles from amplicon and shotgun metagenomic sequence data. The Microbial Metagenomics Analysis Center serves as a point of reference for current best practices in this space and maintains several best-of-breed algorithms for processing metagenomic data to serve the diverse needs of the research community. The center continually monitors advancements, and conducts independent benchmarking, to provide users with state-of-the-art, re-usable, and reproducible solutions for processing metagenomic sequence data and possesses the capability to develop bespoke workflows to meet the needs of individual investigators.

Statistical analyses of microbial community samples

The statistical analysis of microbiome data is inherently complex given next-generation sequencing of community environments returns taxonomic and functional profiles that are high-dimensional (often >1,000 taxa), sparse (most taxa observed in only a subset of samples), and compositional (counts provide no information on absolute abundance). In addition, longitudinal and multiple group study designs introduce challenges not often meet by “off-the-shelf” tools designed for two-group, cross sectional designs. The Microbial Metagenomics Analysis Core provides a single point of entry for investigators requiring rigorous statistical analyses of microbiome data using state-of-the-art approaches that account for the unique features of these data.